Question

1. draw structures illustrating the hydrogen bonding between amide groups of peptide chains
2. what is the configuration of almost all naturally occurring amino acids at the α (alpha) carbon
3. why is an alpha amino acid such as alanine more acidic than a regular carboxyllic acid
4. strecker synthesis Formation dl-phenylalanine
5. outline the steps to synthesize the simple dipeptide AL (think about two amino acids that begin with an A and an L)
6. give the structure and name of the nucleosides in dna and rna
7. give the structure of most lipids of biological origin
8. which fatty acids are found in peanut, corn, and coconut oil

Answer 1

Hydrogen bonding in polypeptides takes place between the amide H and the carbonyl O. These kinds of binds link various polypeptide chains together and variously give rise to alpha-helices and beta-sheets. See attached picture for the bonding indicated by the dashed lines and arrows.

Naturally occuring amino acids all have the L conformation at the alpha carbon atom instead of the D form. The laevorotatory L form (as opposed to the D which is the dextrorotatory form) is the stereoisomer which rotates plane polarized light to the left.

All amino acids have an extra amino group as compared to a regular carboxylic acid. This has an electron-withdrawing inductive effect. Consequently, the O-H bond in amino acids is much more polarised and the deprotonation occurs more easily.

In the Strecker synthesis, the aldehyde reacts with ammonium chloride in the presence of KCN to form an alpha-aminonitrile. This is hydrolysed to form alpha amino acids.

See attached diagram.

To synthesize a dipeptide AL or Ala-Leu we first need to block the carboxylic acid of Leu by adding a methyl ester and also block the free amine group of Ala by addition of Boc to convert to a carbamate. (Boc = butyloxycarbonyl) These blocked or protected amino acids are allowed to react in the presenc of the coupling reagent N,N-dicyclohexylcarbodiimide (DCC) to form the dipeptide product. DCC dehydrates the only available carboxylic acid and amine to form the amide bond. The protective groups are later removed to give the dipeptide. See attached picture for the reaction.